Coexpression cluster:C1635

Full id: C1635_brain_smallcell_occipital_somatostatinoma_temporal_duodenum_small

Phase1 CAGE Peaks

Hg19::chr11:45307817..45307898,-	p1@SYT13
Hg19::chr7:158380402..158380413,-	p7@PTPRN2
Hg19::chr7:158380420..158380433,-	p4@PTPRN2
Hg19::chr7:158380440..158380454,-	p6@PTPRN2
Hg19::chr7:158380468..158380523,-	p2@PTPRN2

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0019198	transmembrane receptor protein phosphatase activity	0.0203930061304151
GO:0005001	transmembrane receptor protein tyrosine phosphatase activity	0.0203930061304151
GO:0005887	integral to plasma membrane	0.0203930061304151
GO:0031226	intrinsic to plasma membrane	0.0203930061304151
GO:0030133	transport vesicle	0.0385377429525907
GO:0044459	plasma membrane part	0.0391926789972099

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
central nervous system	6.76e-40	82
regional part of nervous system	8.56e-39	94
nervous system	8.56e-39	94
neural tube	9.44e-38	57
neural rod	9.44e-38	57
future spinal cord	9.44e-38	57
neural keel	9.44e-38	57
adult organism	7.84e-35	115
regional part of brain	7.51e-33	59
brain	6.42e-32	69
future brain	6.42e-32	69
regional part of forebrain	6.73e-31	41
forebrain	6.73e-31	41
future forebrain	6.73e-31	41
anterior neural tube	1.07e-29	42
neurectoderm	7.31e-29	90
neural plate	9.56e-29	86
presumptive neural plate	9.56e-29	86
telencephalon	3.12e-26	34
gray matter	3.94e-26	34
brain grey matter	3.94e-26	34
regional part of telencephalon	2.45e-25	33
cerebral hemisphere	3.68e-25	32
pre-chordal neural plate	1.60e-22	61
ectoderm	2.08e-22	173
presumptive ectoderm	2.08e-22	173
ectoderm-derived structure	5.59e-22	169
head	1.51e-21	123
regional part of cerebral cortex	7.13e-21	22
anterior region of body	1.02e-20	129
craniocervical region	1.02e-20	129
cerebral cortex	9.35e-20	25
pallium	9.35e-20	25
neocortex	2.87e-19	20
tube	1.82e-16	194
multi-tissue structure	4.59e-16	347
anatomical conduit	7.69e-15	241
organ	9.50e-13	511
organ part	1.72e-12	219
anatomical cluster	1.82e-12	286
embryo	2.13e-12	612
organism subdivision	2.42e-11	365
multi-cellular organism	4.29e-10	659
embryonic structure	4.72e-10	605
developing anatomical structure	4.72e-10	605
germ layer	9.72e-10	604
embryonic tissue	9.72e-10	604
presumptive structure	9.72e-10	604
epiblast (generic)	9.72e-10	604
cell layer	3.43e-09	312
posterior neural tube	3.98e-09	15
chordal neural plate	3.98e-09	15
epithelium	4.48e-09	309
temporal lobe	3.49e-08	7
basal ganglion	4.76e-08	9
nuclear complex of neuraxis	4.76e-08	9
aggregate regional part of brain	4.76e-08	9
collection of basal ganglia	4.76e-08	9
cerebral subcortex	4.76e-08	9
cavitated compound organ	7.24e-08	32
nucleus of brain	8.44e-08	9
neural nucleus	8.44e-08	9
segmental subdivision of nervous system	9.59e-08	13
trunk region element	2.21e-07	107
segmental subdivision of hindbrain	3.28e-07	12
hindbrain	3.28e-07	12
presumptive hindbrain	3.28e-07	12
gastrointestinal system	3.60e-07	35
subdivision of digestive tract	3.95e-07	129
endodermal part of digestive tract	3.95e-07	129
anatomical system	4.45e-07	625
anatomical group	5.68e-07	626

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CHD2#1106	4	8.27521826729349	0.000402837356710173	0.00387616829716729
E2F1#1869	4	3.92591137190346	0.00721498454710636	0.0298662612411907
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0282876662678192
EGR1#1958	4	3.99054327584811	0.006780098300144	0.0287556014769031
ETS1#2113	4	7.78300873776187	0.000512103594768887	0.00443920877606804
HMGN3#9324	4	6.54283817868047	0.0010080127776835	0.00721809026318048
IRF1#3659	4	6.10973100285112	0.00131552526476799	0.00880662413480575
REST#5978	4	7.72002297290242	0.000528636377365057	0.00457114212747386
SIN3A#25942	4	4.32710778145211	0.00497705285576288	0.0232364069379982
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135147062356338
YY1#7528	4	3.92893659988308	0.00719386626991762	0.0298308663290688
ZBTB7A#51341	4	5.88152744630072	0.00152494756104223	0.0097129961778185

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.